PARKLAND, Fla. — Isaah Jean bowed his head in the dimly lit living room of his family’s apartment and prayed for his classmates.

“Help them get through this trying time,” the 14-year-old said, seated on the couch, with his mother kneeling next to him.

To God he pleaded: “I want you to protect us.”

Jean, a freshman at Marjory Stoneman Douglas High School, returned to class Wednesday, hobbling on crutches, one foot in a cast. It was two weeks after police say a former student opened fire in the school with an AR-15, killing 14 classmates and three staff members.

Jean found himself face-to-face with the gunman, who was trying to get into a first-floor classroom. He threw his cellphone at the man and then sprinted from the building, fracturing his foot as he leapt over a stairwell.

The massacre was one of the deadliest school shootings in U.S. history. It brought renewed urgency to the national debate over school safety, with young survivors tearfully calling for changes to gun laws, students walking out of classrooms to protest gun violence, and President Trump urging schools to arm their teachers.

On Wednesday, students came back to a place both familiar and surreal, with armed guards, TV trucks and piles of flowers and homemade memorials outside.

Marjory Stoneman Douglas High School student Isaah Jean, 14, seen at home Monday, returned to school Wednesday. (Matt McClain/The Washington Post)

Students wearing memorial T-shirts snaked their way through crowds of well-wishers, who passed out carnations and held up signs of support. Hundreds of police officers lined entrances to the school, some giving high-fives to students as they passed.

There were support dogs and even ponies painted with “MSD Strong” offering free pony kisses.

Bruna Oliveira, a 14-year-old freshman who saw her favorite teacher shot in the chest, spent the last two weeks in counseling. Wednesday morning, she said she was eager to be among students who would understand what she had been through.

Additional armed guards will patrol the campus for the remainder of the school year.

On Wednesday, the father of one of the victims told CNN about coming back to Stoneman Douglas without his daughter Jaime.

“My son walks in here without his sister,” Fred Guttenberg said. “My daughter’s friends walk in there. They used to always walk in with my daughter . . . and they’re walking in there without her.”

In that CNN interview, Guttenberg spoke directly to Trump, asking him to take action to stop the threats being made against survivors who are calling for gun control. He talked about students being threatened with violence in recent days, and said he hopes law enforcement agencies are investigating those threats to prevent further trauma.

Law enforcement agencies have been criticized for not heeding warnings that the suspected gunman, Nikolas Cruz, was dangerous.

Father of Florida school shooting victim on the threats being made against student survivors: “I need President Trump today to address it publicly and demand that everyone who is making these threats stop… This community has been through trauma… Trump: make an announcement.” pic.twitter.com/iIQPGvA6CV

Students started the day Wednesday in fourth period — the class that was interrupted by gunfire two weeks ago.

Forty therapy dogs roamed the campus, and 150 school counselors stood ready to listen. Many students collected belongings they had left behind in classrooms in the rush to escape.

In class, teachers embraced their students, told them they were grateful they were okay, and allowed students to talk about what had happened. Senior Suzanna Barna said the school received donations of snacks, games, stress balls, “anything to help us cope.”

Barna said students maintained their composure throughout the school day, but it was difficult to ignore the spaces created by classmates who were killed two weeks ago or those still recovering from injuries.

That’s when some students broke down, she said. “When you see the empty desks, it’s real.”

As the day wore on, math teacher Jim Gard said it began to feel like some semblance of normalcy had returned. Gard stationed a counselor in his classroom for students to talk to, juggled stress balls and told bad jokes to cheer up the students.

Students, eager to return to their high-octane academic routines, asked the counselor about SAT’s and Advanced Placement exams.

“They were really ready to go back, to go on with their lives,” Gard said.

Beginning next week, Gard said, he plans to start where they left off, reviewing logarithms and teaching unit circles.

Ninety-five percent of students showed up at the school Wednesday, district Superintendent Robert Runcie said. Only 15 students and four teachers have inquired about switching schools.

“Today was a major milestone for us,” he said. “We took a major step in the recovery process.

“They continue to be inspiring students,” Runcie said. “They continue to show us their resilience. ”

Caesar Figueroa, who has two children attending the school, came Wednesday to thank a teacher.

His 16-year-old daughter, Gabriella, was walking across campus when she heard the barrage of shots and ran upstairs to an adjacent building. She began banging on classroom doors, begging to be let in.

Finally, a math teacher, Kathryn Gilliam, cracked open a door and the girl slipped inside, hiding in a closet until she was rescued by police.

There was no way to ever repay Gilliam, but Figueroa said he had to do something. So, he bought her gift certificates to Starbucks and Olive Garden, and a bouquet of colorful flowers.

“I can’t thank you enough for letting Gabriella in the classroom,” he wrote in the card. “We are truly grateful. You are an outstanding teacher.”

This was just one of many photos taken today! Thanks to the therapy dogs; they have been a major source of healing for my Eagles!🦅🦅 pic.twitter.com/s6pRKDEuAq

Following the shooting, Trump called for teachers to be armed and trained, a suggestion rejected by many educators.

Students continue to demand that lawmakers change gun laws, and several traveled Monday to Washington to speak to members of Congress. Students have pressured companies to end discount programs for NRA members.

Across the country, students who are accustomed to regular lockdown drills to prepare for the possibility of a mass shooting have staged walkouts and issued calls for strengthening gun control laws.

In Parkland, the last two weeks have been punctuated by vigils, marches, funerals for classmates and teachers, and trips to grief counseling. The last of the victims, Martin Duque, a soccer-loving freshman, was laid to rest Sunday.

Alex Wang holds a picture of his brother, Peter Wang, a victim in the shooting at Marjory Stoneman Douglas High School, after his brother’s funeral last week. (Taimy Alvarez/South Florida Sun-Sentinel via AP)

Classes will run only a half day this week, and Principal Ty Thompson said in a tweet to students that they will focus on “emotional readiness and comfort not curriculum.”

Looking forward to tomorrow Eagles! Remember our focus is on emotional readiness and comfort not curriculum: so there is no need for backpacks. Come ready to start the healing process and #RECLAIMTHENEST 🦅🦅🦅🦅

I pray that today is the beginning of our long and difficult journey from grief, sorrow and anger to a new consciousness of hope, compassion and love. Thank you to our young people for leading the way. Welcome Back! #MSDStrong#NeverAgainpic.twitter.com/ytCNfMxwSe